Integrating CCLE RNA-seq and RPPA data.
Data using:
- raw RNA-seq gene counts*
- TPM normalized RNA-seq*
- RPKM normalized RNA-seq
- normalized RPPA*
- Used these datasets for analysis
Data was obtained from CCLE: https://portals.broadinstitute.org/ccle
Names of datasets used (based on v3.1 script):
-
CCLE_RNAseq_genes_counts_20180929.gct (found in CCLE site)
- Raw RNA-seq counts
- used for PCA
-
CCLE_RNAseq_rsem_genes_tpm_20180929.txt (found in CCLE site)
- RNA-seq counts TPM normalized
-
breast_cell_lines_V2.csv (found in metadata folder in github)
- breast cancer cell lines only
- ER positive vs. negative metadata
-
CCLE_RPPA_20181003.csv (found in CCLE site)
- RPPA data
- log2 median-centered
- for more info: https://www.mdanderson.org/content/dam/mdanderson/documents/core-facilities/Functional%20Proteomics%20RPPA%20Core%20Facility/RPPA%20Materials_Methods_2016.pdf
-
CCLE_RPPA_Ab_info_20181226.csv (found in CCLE site)
- RPPA antibody/gene data
Folders in github that are relevant:
- comparison_plots_081420
- plots that compare integrative vs. RNA-seq only pathways
- int_080320
- plots for integrative pathways
- rna_only_080320
- plots for RNA-seq only pathways
- scripts
- R code (use the most current one: v3.1)
- metadata
- extra metadata sets
- presentations
- presentations on methods and results
- lm_FC
- plots for linear model transformation